Ligand profile

19X

Ligand co-crystallized with a similar protein (Protein Data Bank).

Bound to: VK055_4030 — DNA topoisomerase IV, B subunit

Via homolog PDB 4hy1 UniProt A0A0J9WZF0 Formula C₂₀H₁₉ClN₆OS
Mol. weight 426.93 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
19X
PDB
4hy1
UniProt (similar protein)
A0A0J9WZF0
Target protein
VK055_4030

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 426.93 Da
LogP (Crippen) 3.44
H-bond donors 2
H-bond acceptors 6
TPSA 100.26 Ų
Rotatable bonds 4
Aromatic rings 3 / 5
Heavy atoms 29
Fraction sp³ C 0.30
Formula C₂₀H₁₉ClN₆OS

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy Check

Estimated from TPSA and LogP only: TPSA ≤ 90 Ų and −1 ≤ LogP ≤ 5 are treated as a favorable small-molecule permeability screen.

  • TPSA ≤ 90 Ų 100.3
  • −1 ≤ LogP ≤ 5 3.44
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 426.9
  • LogP ≤ 5 3.44
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 100.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCc1c(c2c([nH]1)nc(nc2N3CC[C@H](C3)N)Sc4ccc5c(c4)C(=O)N=C5)Cl
InChI 
InChI=1S/C20H19ClN6OS/c1-2-14-16(21)15-17(24-14)25-20(26-18(15)27-6-5-11(22)9-27)29-12-4-3-10-8-23-19(28)13(10)7-12/h3-4,7-8,11H,2,5-6,9,22H2,1H3,(H,24,25,26)/t11-/m1/s1
InChIKey 
MFHNBYVWNDLIQC-LLVKDONJSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Source
PDB
Binding sites
PF02518

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to VK055_4030.

PDB 19

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 18

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)